How about adding pop-up text to identify the Quirk/code when you hover over a stripe in the Highlights Column?

This would help the user figure out which code(s) has(have) already been applied and is especially important when colors are similar (or even the same) and thus cannot be visually distinguished in the Canvas View.

This would apply to the Home/Canvas View and the Overlap View, as well as in Queries (i.e., basically anywhere the Highlights stripes are shown).

-Ryan

EDIT1: I just noticed that Quirk names appear in the bottom left "status bar" (to the left of the Zoom slider) when you hover over the highlight bars. While this is great and accomplishes the objective of my suggestion, I think pop-ups would provide significant improvement for several reasons:

the distance from mouse pointer to text is large on wide-screen monitors, so it's hard to see which one you are pointing at while reading it on the other side of the screen

the text is small and the contrast is low, which makes the Quirk names hard to notice and read

when viewed using small screens or screens oriented vertically (portrait-mode) rather than horizontally (landscape-mode), that space on the status bar gets covered up by the Zoom slider, especially when the Source pane is wide.
This is why I didn't notice the Quirk names there before.

EDIT2: If pop-ups are infeasible for some reason, then I'd suggest:
- reserving some space on the status bar so that part of the Quirk name is always visible even when the Source pane is fully expanded

- enhancing the text with bold font to help the Quirk names stand out and to distinguish them from the accompanying note about right-clicking the highlight to remove it

- adding mention of the status bar and its variable functions in the User Manual, especially on the figure that shows the Canvas View (section 3.1), where the Zoom slider is labeled and discussed (currently, the status bar isn't mentioned until much later)